Automated analysis of interatomic contacts in proteins

Motivation: New software has been designed to assist the molecular biologis t in understanding the structural consequences of modifying a ligand and/or protein. Results: Tools are described for the analysis of ligand-protein contacts (L PC software) and contacts of structural units (CSU software) such as helice s, sheets, strands and residues. Our approach is based on a detailed analys is of interatomic contacts and interface complementarity. For any ligand or structural unit, these software automatically: (i) calculate the solvent-a ccessible surface of every atom; (ii) determine the contacting residues and type of interaction they undergo (hydrophobic-hydrophobic, aromatic-aromat ic, etc.); (iii) indicate all putative hydrogen bonds. LPC software further predicts changes in binding strength following chemical modification of th e ligand.